Ginsenoside Rg1 (Rg1) is the main bioactive ginseng component. This study investigates the effects of Rg1 on cognitive deficits triggered by chronic sleep deprivation stress (CSDS) and explores its underlying mechanisms. Rg1 effectively improved spatial working and recognition memory, as evidenced by various behavioral tests. RNA-sequence analysis revealed differential gene expression in the metabolic pathway. Treatment with Rg1 abrogated reductions in SOD and CAT activity, lowered MDA content, and increased Nrf2 and HO-1 protein levels. Rg1 administration alleviated hippocampal mitochondrial dysfunction by restoring normal ultrastructure and enhancing ATP activities and Mfn2 expression while regulating Drp-1 expression. Rg1 mitigated neuronal apoptosis by reducing the Bax/Bcl-2 ratio and the levels of cleaved caspase-3. Additionally, Rg1 upregulated AMPK and SIRT3 protein expressions. These findings suggest that Rg1 has potential as a robust intervention for cognitive dysfunction associated with sleep deprivation, acting through the modulation of mitochondrial function, oxidative stress, apoptosis, and the AMPK-SIRT3 axis.